Leaders of the California Institute for Regenerative Medicine are contemplating ways to extend the life of the state’s taxpayer-supported stem cell research funding agency. In the meantime, they are drawing plans for three major initiatives that would pay out hundreds of thousands of dollars in grants and loans to move potential therapies and cures for a wide range of diseases into human clinical trials.

One could follow from the other. If researchers, with the help of CIRM’s largesse, develop therapies or cures for Alzheimer’s, diabetes or other diseases, venture capital firms and drug-development companies — or perhaps even taxpayers who in 2004 approved Proposition 71 to stake the agency with $3 billion — might pony up for CIRM 2.0.

Funding San Francisco-based CIRM past 2017 — when officials expect its last award to be made — is “a front-burner issue,” said Jon Thomas, the former lawyer, investment banker and biologist who heads the agency’s board.

“We believe the work is so valuable by the scientists we’re funding that it behooves us to get projects through” the second phase of the Food and Drug Administration’s three-step drug approval process, Thomas said. Getting there, however, can cause companies to cross some high hurdles.

CIRM’s clock is ticking. Roughly 60 percent of the agency’s ultimate $3 billion pot has been earmarked. At the same time, it is increasingly reaching out to biotech and big pharmaceutical companies as well as the venture capital community to link them to CIRM-funded researchers.

In all, the money has flowed to more than 60 research institutions and companies — including more than $744 million to Bay Area organizations — attacking close to 40 diseases. In fact, Stanford University and the University of California, San Francisco, rank among the top five CIRM awardees.

The money has placed California — and the Bay Area particularly — at the center of the stem cell research universe. It has enticed researchers and companies to locate in the state.

Compared to its early days, when its six-figure grants funded job training or basic research in academic labs then expanded quickly into high-profile lab construction projects, today’s CIRM has evolved into drug and business development. Two CIRM-funded projects are making their way into human trials, and Thomas said three to five more could be tested on humans by the end of 2014.

StemCells Inc. of Newark is one of the companies hoping to leverage CIRM’s cash into a clinical trial. Publicly traded StemCells last year was awarded two forgivable loans from CIRM — each for about $20 million, for an Alzheimer’s program and to expand a spinal cord injury trial — but ultimately rejected the spinal cord award.

“We felt the forgivable loan proposition really enabled us to think of taking on a very, very high-risk program,” said StemCells CEO Martin McGlynn, whose company’s treatments use purified neural stem cells from cells extracted from the brain tissue of aborted fetuses.

Without CIRM’s help in building StemCells Inc.’s Alzheimer’s program, McGlynn said, the company would not be able to advance that work. Now it must deliver an FDA-acceptable application for a human trial within four years.

“Does that mean accelerating it? In this instance, it’s more than that,” McGlynn said. “It’s funding a project that would not be started.”

Still, CIRM awards to companies come with caveats. For one, companies must file an investigational new drug application with the FDA within four years. There also are intellectual property rules and other hurdles that, despite changes by CIRM over the years, companies say shackle them.

Of the $1.8 billion awarded by CIRM to date, only $183.8 million has gone to companies, including $16 million in March to Cellular Dynamics International of Madison, Wis. — a company co-founded by induced pluripotent stem cell pioneer Jamie Thomson, who also is a researcher at UC Santa Barbara — to help set up a stem cell bank at Novato’s Buck Institute for Research on Aging.

Not all of those awards have been paid out or used. Besides StemCells Inc.’s decision not to use CIRM cash to expand its spinal cord trial, Geron Corp. received $6.4 million of a $25 million loan awarded in 2011 but returned all the money plus interest after ending a trial in patients with fresh spinal cord injuries, and StemCells Inc. turned down a $20 million CIRM award that would have expanded its spinal cord injury trial.

For many companies, the cost of playing with CIRM is too much. Besides Prop. 71’s requirement that California citizens receive a discount on therapies ultimately derived from CIRM awards, the IP rules can put companies in a pinch when seeking funders or partners who prefer a clear title on IP.

BayBio, northern California’s biotech industry trade organization, has pushed for CIRM to relax some of its stringent rules.

CIRM awards to companies are structured as forgivable loans — unlike grants that are awarded to academic researchers.

“Our hope was that CIRM would provide risk capital to companies such as ours that were struggling through the valley of death,” McGlynn said, referring to the period when biotech companies have promising experimental therapies but little cash.

Instead, it took eight years from the passage of Prop. 71 until StemCells was awarded money. Even then, the IP rules caused confusion among investors, McGlynn said.

“They’re not insurmountable. They can be managed,” McGlynn said. “They create challenges and obstacles to bringing in partners and other investors.”

CIRM’s rules are evolving. Just last month, CIRM’s board adopted changes, including how the “first commercial sale” — a trigger for sharing revenue with CIRM — is defined.

“We’re trying to make this industry-friendly,” Thomas said.

At the same time, CIRM’s three major initiatives — the $32 million stem cell bank at the Buck Institute, a $70 million plan to set up six to eight “alpha clinics” to operate human clinical trials and a $40 million DNA sequencing initiative — are prime focuses. So, too, is the agency’s future.

CIRM is paying James Gollub Associates of Tiburon a reported $150,000 to help the agency map its structure. That could mean another bond measure, a public-private venture, venture philanthropy or other arrangement. Those discussions could be helped by ongoing CIRM efforts to link deep-pocketed drug makers and venture capitalists with CIRM-funded projects earlier in the drug-development process. Next month, CIRM will host its third annual “Meeting on the Mesa,” a three-day San Diego meet-up for stem cell researchers and potential funders.

“We’re very much trying to increase the role of industry in what we do,” Thomas said

If a new version of CIRM develops, its leaders must decide within the next two years how it will be structured in order to ensure a flow of cash necessary to push products toward commercialization.

But, Thomas said, there is no certainty of a new source of CIRM funds.

“If there is no new money, we want as much (as possible in the clinic) for the big guys to carry on,” he said.